Table 1.

List of 20 protein atom types and 12 RNA atom types used in ITScore-PR, in which ‘*’ stands for any residue name of proteins

Numbers	Symbol	Atom name
Protein
1	C2+	ARG_CZ
2	C2-	ASP_CG, GLU_CD
3	C2M	*_C
4	C2S	ASN_CG, GLN_CD
5	Car	HIS_CD2, HIS_CE1, HIS_CG, PHE_CD1, PHE_CD2, PHE_CE1, PHE_CE2, PHE_CG, PHE_CZ, TRP_CD1, TRP_CD2, TRP_CE2, TRP_CE3, TRP_CG, TRP_CH2, TRP_CZ2, TRP_CZ3, TYR_CD1, TYR_CD2, TYR_CE1, TYR_CE2, TYR_CG, TYR_CZ
6	C3C	ALA_CB, ARG_CB, ARG_CG, ASN_CB, ASP_CB, GLN_CB, GLN_CG, GLU_CB, GLU_CG, HIS_CB, ILE_CB, ILE_CD1, ILE_CG1, ILE_CG2, LEU_CB, LEU_CD1, LEU_CD2, LEU_CG, LYS_CB, LYS_CD, LYS_CG, MET_CB, PHE_CB, PRO_CB, PRO_CG, THR_CG2, TRP_CB, TYR_CB, VAL_CB, VAL_CG1, VAL_CG2
7	C3A	*_CA
8	C3X	ARG_CD, CYS_CB, LYS_CE, MET_CE, MET_CG, PRO_CD, SER_CB, THR_CB
9	N2N	ALA_N, ARG_N, ASN_N, ASP_N, CYS_N, GLN_N, GLU_N, GLY_N, HIS_N, ILE_N, LEU_N, LYS_N, MET_N, PHE_N, PRO_N, SER_N, THR_N, TRP_N, TYR_N, VAL_N
10	N2+	ARG_NH1, ARG_NH2
11	N2X	ASN_ND2, GLN_NE2
12	Nar	HIS_ND1, HIS_NE2, TRP_NE1
13	N21	ARG_NE
14	N3+	LYS_NZ
15	O2M	*_O
16	O2S	ASN_OD1, GLN_OE1
17	O3H	SER_OG, THR_OG1, TYR_OH
18	O2-	ASP_OD1, ASP_OD2, GLU_OE1, GLU_OE2
19	S31	CYS_SG
20	S30	MET_SD
RNA
1	C2X	C_C2, G_C6, U_C2, U_C4
2	Car	C_C4, C_C5, C_C6, G_C2, U_C5, U_C6, A_C2, A_C4, A_C5, A_C6, A_C8, G_C4, G_C5, G_C8
3	C3X	A_C1’, A_C2’, A_C3’, A_C4’, A_C5’, C_C1’, C_C2’, C_C3’, C_C4’, C_C5’, G_C1’, G_C2’, G_C3’, G_C4’, G_C5’, U_C1’, U_C2’, U_C3’, U_C4’, U_C5’
4	N2N	C_N1, G_N1, U_N1, U_N3
5	N2X	A_N6, C_N4, G_N2
6	Nar	C_N3, G_N3, A_N1, A_N3, A_N7, G_N7
7	N21	A_N9, G_N9
8	O2	C_O2, G_O6, U_O2, U_O4
9	O31	A_O2’, C_O2’, G_O2’, U_O2’
10	O32	A_O3’, A_O4’, A_O5’, C_O3’, C_O4’, C_O5’, G_O3’, G_O4’, G_O5’, U_O3’, U_O4’, U_O5’
11	O2-	A_OP1, A_OP2, C_OP1, C_OP2, G_OP1, G_OP2, U_OP1, U_OP2
12	P	A_P, C_P, G_P, U_P